title: ALL_54_BS

city: UNSW Sydney

first: Yizhou

last: Huang

state: NSW

address: High Street

country: Australia

institute: University of New South Wales

description: Basal DNA methylation of ALL54

data_processing:
Low quality reads and adaptor sequences were removed using Trimmomatic (version 0.36) using the parameters LEADING:28 TRAILING:28 SLIDINGWINDOW:4:28 MINLEN:50
Alignment was performed using Bismark (version 0.16.1) with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files. Aligned files for UCSC genome browser visualization.

source_name: ALL xenograft cells

growth_protocol: ALL xenograft cells were inoculated by tail-vein injection into NOD/SCID mice, and engraftment was monitored weekly. When >70% %huCD45+ engraftment in the peripheral blood was apparent, which occurred 8-10 weeks post-transplantation, mice were culled and cell suspensions of spleens were prepared and mononuclear cells enriched to >97% human by density gradient centrifugation.

extract_protocol:
Genomic DNA was extracted using QIAGEN DNA extraction kit according to manufacturer's instruction.
Library was prepared by Novogene (Hong Kong) for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: ALL xenograft cells

tag: xenograft id

tag: data type

value: Methylation


title: ALL_50_BS_Meth

status: Public on Nov 08 2019

type: SRA

description: Basal DNA methylation of ALL50

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue


title: ALL54_Ctrl_ATAC

description: ATAC-seq of ALL54 Control

data_processing:
Raw sequencing reads filtered for adapter contamination, low quality scores, and excluded reads in which more than 10% of bases were unknown.
Filtered paired-end ATAC-seq reads aligned to the human genome (hg19) using the software package STAR with standard parameters.
Filtered single-end ATAC-seq reads aligned to the human genome (hg19) using the software package BWA with standard parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files. Aligned files for UCSC genome browser visualization.

growth_protocol: ALL xenograft cells were inoculated by tail-vein injection into NOD/SCID mice, and engraftment was monitored weekly.

extract_protocol:
Cell suspensions of spleens were prepared and mononuclear cells enriched to >97% human by density gradient centrifugation. The spleen-harvested cells were used for ATAC-seq assay.
Buenrostro, J.D., Wu, B., Chang, H.Y. & Greenleaf, W.J. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol 109, 21 29 21-29 (2015).

treatment_protocol: When >70% %huCD45+ engraftment in the peripheral blood was apparent, which occurred 8-10 weeks post-transplantation, mice were treated with either dexamethasone (15 mg/kg) or vehicle control by intra-peritoneal (IP) injection, and culled at 8 hours following the treatment.

tag: treatment

value: vehicle


title: ALL19_Ctrl_ATAC

description: ATAC-seq of ALL19 Control


title: ALL50_Ctrl_ATAC

description: ATAC-seq of ALL50 Control


title: RNA-seq HA-∆264-1E9 rep4

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

country: USA

institute: Vanderbilt University Medical Center

description:
processed data file: Lance-RAMOS.count
delta264-1E9-4

library_source: transcriptomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Reads with mapping quality less than 10 were removed.
Peaks were called by MACS2.
Differential binding peaks were identified using DiffBind based on consensus peaks occurring at least two samples.
After adapter trimming and low quality sequence removal by cutadapt, PRO-seq reads longer than 15bp were reversed complemented using FastX tools.
Reverse complements of the trimmed reads were aligned to the human genome hg19 using Bowtie2.
Reads mapped to rRNA loci and reads with mapping quality less than 10 were removed.
Bam files were given to NRSA (http://bioinfo.vanderbilt.edu/NRSA/) to estimate RNA polymerase abundance in proximal-promoter and gene body regions of genes, to calculate pausing index and pausing index alterations, and to detect enhancers and quantify eRNA changes.
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content:
ChIP-seq: one peak file per Sample
PRO-seq: text file with raw counts for promoter-proximal and gene body region, and density for gene body (ppc, gbc, gbd)
RNA-seq: tab-delimited text file include raw counts for each Sample

molecule: total RNA

source_name: RNA-seq HA-∆264-1E9

growth_protocol: Ramos cells were maintained in RPMI1640 +10 % FBS, Pen/Strep, and 50 ug/ml Hygromycin B. Puromycin was added to 200 ng/ml for WT, WBM, and ∆264 cells.

extract_protocol:
Chromatin was clarified from sonicated cells and protein-DNA complexes were isolated with antibody.
ChIP libraries were prepared according to New England Biolabs  instructions accompanying the NEBNext Ultar II DNA Library Prep Kit for Illumina (Part# E7645S). After adapter ligation DNA was PCR amplified with NEBNext Multiplex Oligos for Illumina (Part# E7335S and E7500S) for 16 cycles (HA ChIP) or 15 cycles (WDR5 ChIP). For RNA-seq, libraries  were prepared using Poly-A selected at Genewiz using their standard methods, and for PRO-Seq, libraries were made using RNA that was made through a biotin-run on reaction.Biotin-RNA was base hydrolyzed, and extracted. 3'-adaptors were ligated to ends and 5'caps were removed, repaired, and then 5'-adaptors were ligated as well. Purified and intact biotin-RNA containing adaptors was used in a reverase transcriptase reaction to generate cDNA and cDNA was used to amplify full library using NEB High Fidelity Phusion polymerase.RNA libraries were prepared using Poly-A selected RNA.

treatment_protocol: Cells were plated at 0.75 million in RPMI +10% FBS + Pen/Strep and treated with 20 nM 4-OHT for 24 h

tag: cell line

value: Ramos

tag: cell type

value: Burkitt's lymphoma cell line

tag: genotype/variation

value: Tumor derived {delta}264-HA

value: 48h post 4-OHT treatment


title: ALL10_Ctrl_ATAC

description: ATAC-seq of ALL10 Control


title: ALL2_Dex_ATAC

description: ATAC-seq of ALL2 Dex

value: Dex


title: ALL7_Dex_ATAC

description: ATAC-seq of ALL7 Dex


title: ALL7_Ctrl_ATAC

description: ATAC-seq of ALL7 Control


title: ALL8_Dex_ATAC

description: ATAC-seq of ALL8 Dex


title: ALL54_Dex_ATAC

description: ATAC-seq of ALL54 Dex


title: ALL2_Ctrl_ATAC

description: ATAC-seq of ALL2 Control


title: ALL50_Dex_ATAC

description: ATAC-seq of ALL50 Dex


title: ALL8_Ctrl_ATAC

description: ATAC-seq of ALL8 Control


title: ALL26_Dex_ATAC

description: ATAC-seq of ALL26 Dex


title: RNA-seq HA-WT-3E7 rep4

description:
processed data file: Lance-RAMOS.count
WT-3E7-4

source_name: RNA-seq HA-WT-3E7

value: Tumor derived WT-HA


title: ALL26_Ctrl_ATAC

description: ATAC-seq of ALL26 Control


title: ALL16_Dex_ATAC

description: ATAC-seq of ALL16 Dex


title: ALL11_Dex_ATAC

description: ATAC-seq of ALL11 Dex


title: ALL11_Ctrl_ATAC

description: ATAC-seq of ALL11 Control


title: RNA-seq HA-WT-3E7 rep1

description:
processed data file: Lance-RAMOS.count
WT-3E7-1


title: ALL10_Dex_ATAC

description: ATAC-seq of ALL10 Dex


title: ALL19_Dex_ATAC

description: ATAC-seq of ALL19 Dex


title: KT25-Treg

city: Los Angeles

first: Richard

middle: Sungho

last: Ahn

state: CA

address: 611 Charles E. Young Drive East, UCLA, Boyer Hall, 510C

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California Los Angeles

data_processing:
Read quality was checked using FastQC v. 0.11.4
Reads with adapter contamination were trimmed using Trimmomatic v. 0.32
Reads aligned using STAR vs. 2.4.2a
FPKMs and differential expression tests calculated using the Cufflinks Suite v. 2.2.1.
Gene annotations obtained from RefSeq
Genome_build: hg19
Supplementary_files_format_and_content: CSV file containing a matrix of FPKM values for all samples.

molecule: polyA RNA

source_name: Keratinocytes

extract_protocol:
RNA was extracted from biopsy samples using the Qiagen Allprep DNA/RNA mini kit.
The Ovation RNA-seq System V2 protocol was implemented to amplify cDNA from 500 pg of qualified mRNA from each sample. cDNA amplification was performed using NuGEN Ribo-SPIA technology. The cDNA was then sheared as ~200 bp fragments, end-repaired, followed by A-tailing and adapter ligation reactions. The library was PCR enriched and purified using the Ampure XP bead size selection method.

value: skin

value: keratinocyte

tag: cell subtype

value: CD4+ Treg cells


title: KT09-Treg


title: KT14-Treg


title: KT18-Treg


title: melanoma1_Teff

city: San Francisco

first: Margaret

last: Lowe

address: 513 Parnassus Avenue, HSW1201B

institute: UCSF

data_processing:
Following clipping of adapter sequences, reads were aligned to Ensembl hg19 GRCh37.75 with Tophat (v 2.0.12)
SAM files were generated with SAMtools from alignment results
Reads were counted with htseq-count 0.6.1p1 with the union option and -stranded=no
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing raw read counts for each gene

source_name: melanoma skin lesion 1

growth_protocol: Cells were sort-purified from collagenase-digested human melanoma tumors

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Spin Columns
cDNA was created using the SMARTer Ultra Low input kit, sequencing 50 bp paired end unstranded reads

tag: sort purification strategy

value: Cells were sort-purified as live, singlet, CD45+, CD3+, CD4+CD8- CD25+CD27+


title: melanoma2_Treg

source_name: melanoma skin lesion 2

value: Cells were sort-purified as live, singlet, CD45+, CD3+, CD4+CD8- CD25-CD27-


title: melanoma1_Treg


title: Arg2 Treg 3

data_processing:
Following clipping of adapter sequences, reads were aligned to Ensembl hg19 GRCh37.75 with Tophat (v 2.0.12)
SAM files were generated with SAMtools from alignment results
Reads were counted with htseq-count 0.6.1p1 with the union option and -stranded=reverse
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing raw read counts for each gene

source_name: expanded human Tregs

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Spin Columns
cDNA was created using the TruSeq Stranded mRNA input kit, sequencing 50 bp paired end stranded reads

value: Arg2 gRNA pool


title: Scr Treg 2

value: scrambled gRNA


title: PSOTeff5

source_name: psoriatic lesion

growth_protocol: Cells were sort-purified from collagenase-digested human skin

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Spin Columns
cDNA was created from 220 pg of input RNA using the SMARTer Ultra Low input kit, sequencing 50 bp paired end unstranded reads

value: Cells were sort-purified purified as live, singlet, CD45+, CD3+, CD4+CD8- CD25-CD27-

tag: diagnosis

value: psoriasis

value: Teff


title: Arg2 Treg 1


title: melanoma2_Teff


title: PSOTeff1


title: Scr Treg 3


title: Arg2 Treg 2


title: PSOTeff2


title: PSOTeff4


title: NormalTeff2

source_name: healthy human skin

value: healthy


title: NormalTeff4


title: NormalTeff5


title: NormalTeff3


title: NormalTeff1


title: PSOTreg4

value: Treg


title: PSOTreg5


title: PSOTreg3


title: PSOTreg2


title: Scr Treg 1


title: PSOTreg1


title: NormalTreg3


title: NormalTreg1


title: NormalTreg2


title: NormalTreg5


title: NormalTreg4


title: ALL16_Ctrl_ATAC

description: ATAC-seq of ALL16 Control

value: ALL xenograft cells

value: vehicle


title: X5801106023_E

type: RNA

city: Rochester

first: Sean

last: Dowdy

state: Minnesota

address: 200 First St. SW

department: Obstetrics and Gynecology

institute: Mayo Clinic

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina Genome Studio for raw vaules.  R for normalized values.

source_name: FFPE Ovarian Cancer

label_protocol: not provided

extract_protocol: Using FFPE tumor, three 1mm cores were obtained from areas containing >70% tumor nuclei. Total RNA was isolated from these cores using a Qiagen AllPrep DNA/RNA FFPE kit according to the manufacturer's protocol using a Qiacube robot

value: ovarian cancer

tag: tissue preparation

value: FFPE

value: standard

value: mesenchymal

value: SUB-OPTIMAL

value: III

value: serous

tag: newgrade

tag: age

tag: plate


title: X5800744058_K

value: OPTIMAL


title: X5800744060_E

value: differentiated


title: X5800744036_D

value: bevacizumab


title: Huh7-Lunet II

city: Heidelberg

first: Marco

last: Binder

address: Im Neuenheimer Feld 280

department: F170 Virus-Associated Carcinogenesis

country: Germany

institute: German Cancer Research Center (DKFZ)

description: highly permissve Huh7 subclone

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip HG-U133Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the Affymetrix Gene Expression Analysis Technical Manual

scan_protocol: Arrays were scanned in the GeneArray scanner 2500 (Agilent, Palo Alto, CA)

data_processing: The data were analyzed with MAS 5.0 using Affymetrix default analysis settings and global scaling to a target intensity of 1000. RMA analysis was done by RMAexpress software

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix Gene Expression Analysis Technical Manual starting from 13.5µg total RNA. Double-stranded cDNA was synthesized using an T7-oligo d(T)24 primer [5'-GCATTAGCGGCCGCGAAATTAATACGACTCACTATAGGGAGA-(dT24)-3'] (MWG Biotech, Munich, Germany). After generation of double-stranded cDNA from the first-strand cDNA, biotinylated cRNA was synthesized by in vitro transcription using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, New York, NY)

growth_protocol: normal cell culture conditions, 37°C, 95% humidity, 5% CO2, DMEM complete with 10% FCS, 100 µg/mL Pen/Strep and 1x MEM-NEAAs

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

value: human hepatocellular carcinoma

tag: relative hcv permissiveness


title: X6828280034_L

value: proliferative


title: X6828301015_C


title: Huh7 passage 163

description: high passage, highly permissive Huh7 passage

source_name: Huh7 passage 163


title: X5801106022_L

value: II


title: X5800701029_A

value: IV


title: X5800744060_C

value: other


title: X6828280001_C

value: Inoperable


title: Huh7 passage 13

description: low passage, low permissive Huh7 passage

source_name: Huh7 passage 13


title: Huh7-Lunet NP

description: highly permissive Huh7 subclone, rendered non-permissive during passaging (unknown reasons)

source_name: Huh7-Lunet NP


title: X5800744040_H


title: Huh7 passage 154

source_name: Huh7 passage 154


title: X5800744040_F

value: immunoreactive


title: X5801106019_C

value: ovarian cancer


title: X5800744042_I

value: FFPE


title: Huh7 passage 28

source_name: Huh7 passage 28


title: Huh7/5-2

description: highly permissve Huh7 subclone


title: X5800744040_D


title: Huh7-Lunet I

description: highly permissve Huh7 subclone


title: X5800701029_K


title: X5800744025_C

value: standard


title: X5801106023_G


title: X5800744036_L


title: X5800744060_H


title: X5800744041_C


title: X5800744025_L


title: X5800744036_A


title: X5800744042_G

value: mesenchymal


title: X5800744058_F


title: X5800744014_L


title: X5800744041_L


title: X5800701029_F


title: X5800701029_H


title: X5800701019_G


title: X5800744041_E


title: X5800701030_C


title: X5800744007_C


title: X5800744041_I

value: SUB-OPTIMAL


title: X5800744060_I

value: III


title: X5801106019_B

value: serous


title: X5800744005_G

value: OPTIMAL


title: X5800744040_J

value: differentiated


title: X6828280001_E


title: X5800744041_D


title: X5800744019_F

value: bevacizumab


title: X5800744025_A


title: X5800744020_A


title: X5800744041_J


title: X5800744041_G


title: X5800744060_A


title: X5800744036_J


title: X5800701019_B


title: X5800744004_J


title: X5800744041_H


title: X5800701030_A


title: X5800701019_L


title: X5800701030_I


title: X6828301015_B


title: X5801106023_B

value: I


title: X5800744060_B


title: X5800744020_G


title: X5800701019_J


title: X5800744036_E


title: X5800744042_F


title: X5801106022_K


title: X5800710052_F


title: X5800701030_E

value: proliferative


title: X5800744020_F


title: X5800710047_J


title: X5801106019_G


title: X5800744041_B


title: X5800744004_F


title: X5800744004_A


title: X5800710052_L


title: X5801106022_D


title: X5800744019_G


title: X5800701027_K


title: X5800744004_K


title: X5800701027_F


title: X5800744020_E


title: X5800710052_A


title: X5800701010_J


title: X5801106019_H

value: II


title: X5800744007_K


title: X5800744004_L


title: X5800710047_E


title: X5800710041_G


title: X5800744005_E


title: X5800744005_A


title: X5801106019_E


title: X5800710047_H


title: dCAR2_A

city: Beijing

first: Wang

last: Yao

address: No. 28, fuxing street

country: China

institute: Chinese general PLA hospital

description: CAR T treatment by DNMTi inhibitor coculture with Raij

data_processing:
base calling: bcl2fastq  v2.2.0
cutadapt v1.15: cutadapt -a AGATCGGAAGAGC -A AGATCGGAAGAGC -m $length -o ${samplename}_1.cutadapt.fq.gz -p ${samplename}_2.cutadapt.fq.gz $read1 $read2
fastqc v0.11.5; fastx_toolkit v0.0.14: fastqc -f fastq $read1 -o $outdir;  fastx_quality_stats -i $samplename.1.fastq -o $samplename.1_quality_stat.txt
STAR  v2.6.1a: STAR --runThreadN $starThreads --outSAMattributes All --genomeLoad LoadAndKeep --genomeDir $refSTAR -  -readFilesIn $read1 $read2 --readFilesCommand zcat
STAR  v2.6.1a; samtools v1.7: star --genomeDir ./ --runMode genomeGenerate --genomeFastaFiles $reffasta --sjdbFileChrStartEnd SJ.out.tab.* --sjdbOverhang `expr $readlength - 1` --runThreadN $starThreads;   samtools index $samplename\_Aligned.sortedByCoord.out.bam
STAR  v2.6.1a: star --runThreadN $starThreads --outSAMattributes All --genomeLoad LoadAndKeep --genomeDir ../GenomeForPass2 --readFilesIn $read1 $read2 --outFileNamePrefix ${samplename}_ --chimSegmentMin 20 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --limitBAMsortRAM 200000000000
StingTie v1.3.3b: stringtie -p $thread -G $refgtf -o $samplename.gtf -l $samplename $bamfile
Genome_build: Homo_sapiens.GRCh38.94
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were collected from patients by leukapheresis. Primary T cells derived from the PBMCs were activated using Dynabeads Human T-Activator CD3/CD28 magnetic beads (Invitrogen) at a 1:1 bead:cell ratio and cultured in X-VIVO 15 medium (Lonza) supplemented with 300 U/ml recombinant human IL-2 (PeproTech). After 2 days, RetroNectin-coated plates (Takara) were loaded with viral supernatants by centrifuging the plates at 2,000 g for 2 h at 32 °C. Activated T cells were added to the plates and centrifuged at 800 g for 10 min, and Polybrene (Sigma) was added to increase infection efficiency. The following day, the transduced cells were collected and transferred to new flasks for further expansion. The Dynabeads were magnetically removed 2 days after initiating T cell transduction, and the cells were cultured at 106 cells per ml in X-VIVO 15 medium supplemented with 300 IU/mL IL-2, with fresh IL-2-containing medium added every 2 days until the cells were harvested on days 8-10.

extract_protocol:
T cells were resuspended in 250ul PBS and placed in 750ul TRIzol LS (Invitrogen). RNA was extracted using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol. Total RNA integrity was checked using the Bioptic Qsep100 (BIOptic) and quantified using a Synergy H1 (BioTek).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: dCAR and CAR7 T cells were cocultured with Raji cells for 24 h, followed by magnetic selection of CD3+ cells (Miltenyi Biotec).

value: T cell

tag: genotype


title: dCAR4_A

value: CAR T treatment by DNMTi inhibitor coculture with Raij


title: dCAR5_A


title: X5800744042_B


title: X5800744007_D


title: X6828280034_K

value: other


title: X5800701030_K


title: X5800744014_G

value: IV


title: X5800710047_K

value: ovarian cancer


title: X5800744040_B

value: FFPE


title: X5800701030_D


title: X5800744004_D

value: immunoreactive


title: X5801106023_H


title: X5800701030_L


title: X5800701010_E

value: mesenchymal


title: X5800744007_B


title: X5800744014_I

value: standard


title: X5801106019_K


title: X5800710038_G


title: X5800744005_F

value: III


title: dCAR3_A


title: X5800744019_K

value: serous


title: X5800744020_H

value: OPTIMAL


title: X5800701010_L

value: differentiated

value: SUB-OPTIMAL


title: X5800701030_B


title: X5800744004_E

value: bevacizumab


title: X5800710047_D


title: CAR4_A

description: Control CAR after coculture with Raij

value: Control CAR after coculture with Raij


title: dCAR1_A


title: CAR5_A

description: Control CAR after coculture with Raij


title: CAR2_A

description: Control CAR after coculture with Raij


title: CAR1_A

description: Control CAR after coculture with Raij


title: dCAR5

description: CAR T treatment by DNMTi inhibitor

value: CAR T treatment by DNMTi inhibitor


title: dCAR3

description: CAR T treatment by DNMTi inhibitor

value: T cell


title: dCAR2

description: CAR T treatment by DNMTi inhibitor


title: dCAR1

description: CAR T treatment by DNMTi inhibitor


title: CAR5

description: Control CAR

value: Control CAR


title: CAR4

description: Control CAR


title: CAR3

description: Control CAR


title: CAR1

description: Control CAR


title: CAR2

description: Control CAR


title: X5801106022_G


title: X6828280034_C


title: dCAR4

description: CAR T treatment by DNMTi inhibitor


title: X5800744005_I


title: X5800744020_D


title: X5800744014_B


title: Basline-29

city: Sydney

first: Fatemeh

last: Vafaee

state: UNSW

address: Gate 11 Botany Street, UNSW Sydney, School of BABS

department: School of Biotechnology and Biomolecular Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Data pre-processing was performed using a pipeline comprising of adapter trimming (cutadapt), followed by genome alignment to human genome hg 19 using Bowtie (18 bp seed, 1 error in seed, quality score sum of mismatches<70). Where multiple best strata alignments existed, tags were randomly assigned to one of those coordinates. Tags were annotated against mirBase 20 and filtered for at most one base error within the tag.
Counts for each miRNA were tabulated and adjusted to counts per million miRNAs passing the mismatch filter.
Supplementary_files_format_and_content: All samples achieved miRNA read counts >45,000 read counts and miRNAs with low abundance (<50 read counts across more than 20% of samples) were removed.
Supplementary_files_format_and_content: Preprocessed and Filtered read counts

extract_protocol:
Exosomes were isolated from 1 mL RNase A (37 °C for 10 min; 100 ng/ml; Qiagen, Australia) treated serum, by size exclusion chromatography (qEV iZONE Science). Then, Serum exosomes were processed for RNA extraction using the Plasma/Serum Circulating & Exosomal RNA Purification Mini Kit (Norgen Biotek, Cat. 51000) according to the manufacturer’s protocol.
Exosome RNA sequencing libraries were then constructed using the NEBNext Multiplex Small RNA Library Prep Kit for Illumina (BioLabs, New England) according to the manufacturer’s instructions.

value: Fingolimod


title: X5801106022_I

value: other


title: 6Months-28


title: X5800744020_C

value: ovarian cancer

value: IV


title: X5800710052_K

value: FFPE

value: I


title: X5800701019_A

value: standard


title: X5800701030_H

value: proliferative

value: III


title: X5800744007_F

value: OPTIMAL

value: serous


title: X5800710029_L


title: CAR3_A

description: Control CAR after coculture with Raij


title: X5800710041_H

value: immunoreactive


title: X5800710052_J


title: Basline-28

value: No treatment


title: 6Months-27


title: X5800710047_B

value: bevacizumab

value: II


title: X5800710047_A

value: mesenchymal


title: 6Months-26


title: Basline-26


title: X5800744036_H


title: 6Months-25


title: 6Months-24


title: Basline-25


title: Basline-24


title: 6Months-23


title: Basline-23


title: Basline-22


title: 6Months-22


title: Basline-21


title: 6Months-20


title: Basline-20


title: X5801106019_I


title: X6828280034_I

value: SUB-OPTIMAL


title: X5800710009_J

value: Inoperable


title: X5800701019_I

value: other


title: X5800710041_B

value: ovarian cancer

value: differentiated


title: X5800744020_J

value: FFPE


title: X5800744040_I


title: X5800710041_L


title: X5800744058_I


title: X5800710029_D

value: I


title: 6Months-21

value: Fingolimod


title: 6Months-19


title: Basline-19


title: X5800744040_E

value: standard

value: proliferative


title: X5800710029_C

value: OPTIMAL

value: IV


title: X5800710009_H

value: III

value: serous


title: X5800744058_C

value: bevacizumab


title: Basline-18

value: No treatment


title: 6Months-18


title: X5800710029_E


title: X5800744004_H


title: X5800710009_E


title: Basline-17


title: X5800710008_B

value: immunoreactive


title: 6Months-16


title: Basline-16


title: X5800744058_E


title: X5800701010_G

value: SUB-OPTIMAL


title: X5800701019_C


title: 6Months-15


title: X5800710007_K

value: mesenchymal


title: X5800744019_E


title: X5801106023_K


title: Basline-15


title: Basline-14


title: Basline-13


title: X5800744042_C


title: X5800701010_B

value: other


title: 6Months-17


title: 6Months-12


title: X5800710008_E

value: ovarian cancer

value: II


title: 6Months-11


title: Basline-12


title: X5800710008_A

value: FFPE


title: X5800710008_F


title: 6Months-14


title: Basline-11


title: 6Months-9


title: X5800744020_K


title: X5800710008_H

value: differentiated


title: X5800744005_D


title: Basline-9


title: 6Months-8

value: Fingolimod


title: X5800744019_J


title: X5800744005_C


title: X5800701010_K

value: standard


title: X5800744005_K

value: proliferative


title: Basline-8


title: X5800710008_C

value: OPTIMAL


title: 6Months-10


title: 6Months-7


title: X5800744020_L

value: IV


title: 6Months-5


title: Basline-6


title: Basline-7


title: Basline-10


title: X5800744025_F


title: 6Months-4


title: X6828280034_B

value: III


title: X5800744040_A

value: I


title: X5800744007_G


title: X5800701006_L

value: serous


title: X5800710016_B


title: Basline-3

value: No treatment


title: 6Months-2


title: 6Months-6


title: Basline-5


title: 6Months-1


title: Basline-1


title: X5800701010_H


title: X5800710016_I

value: bevacizumab

value: immunoreactive


title: X5800710041_J


title: X5800710009_I


title: Basline-4


title: X5800744005_H


title: X6828280034_A


title: NegA_1

city: Bath

first: Keith

middle: William

last: Vance

state: Somerset

address: University of Bath

department: Department of Biology and Biochemistry

country: United Kingdom

institute: University of Bath

data_processing:
quality and adaptor trimming using trim_galore
merging of paired end reads using flash
in silico dpn2 digestion with dpnIIE.pl
alignment to reference genome with bowtie
bam files are mapped to hg19GENCODEV19.gtf and analysed with DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimitted text file of ENST transcripts and counts in each replicate

source_name: Melanoma cells

growth_protocol: SKMEL28 were grown in DMEM media containing FBS. They were passaged every 3-4 days.

extract_protocol: RNA was extracted using GeneJET RNA purification Kit

treatment_protocol: SKMEL28 were transfected with ASOs targeting DIRC3 and IGFBP5 using lipofectamine.

tag: strain

value: Melanoma

tag: passages


title: NegA_4


title: NegA_2


title: Basline-2


title: X5800744007_I


title: Dirc3_4


title: Igfpb5_2


title: Igfbp5_1


title: Igfbp5_4


title: X5800710047_G

value: mesenchymal


title: X5800744036_C

value: ovarian cancer

value: other


title: X5800710038_A

value: FFPE

value: II


title: X5800710052_G


title: X5800710047_F


title: Dirc3_1


title: X5800710002_G


title: X5800744025_K


title: X5800701027_E


title: Dirc3_2


title: X5800744025_I

value: differentiated

value: SUB-OPTIMAL


title: RNA-Seq_patient_10_primary

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
RNA-Seq results were trimmed to remove 3' A-stretches originating from the library preparation and poor quality reads were filtered out (minimum 97% of bp over quality cutoff 10).
Reads were aligned to the hg19 genome using Tophat.
Data analysis was performed using HOMER (http://homer.ucsd.edu/homer/) and the differential gene expression usign edgeR
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression values (RPKM) and UCSC Bedgraphs are provided

source_name: High grade serous ovarian cancer_primary tumor

growth_protocol: Patient samples were extracted during surgery and snap frozen in liquid nitrogen

extract_protocol:
RNA was purified using Trizol (Thermo Fisher Scientific) and depleted from rRNAs using  Ribo-Zero Gold Kit (Illumina)
The RNA was base-hydrolyzed, dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 11 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

tag: subject status

value: High grade serous ovarian cancer

tag: subject id

tag: tissue type

value: primary tumor

tag: molecule subtype

value: rRNA-depleted RNA


title: RNA-Seq_patient_9_primary


title: X5800701006_J

tag: tissue

tag: treatment

value: III


title: RNA-Seq_patient_8_primary


title: RNA-Seq_patient_8_omentum

source_name: High grade serous ovarian cancer_metastatic tumor

value: metastatic tumor


title: X6828301015_D

value: standard

value: OPTIMAL


title: X5800710001_H

value: serous


title: RNA-Seq_patient_7_omentum


title: X5800710052_H


title: X5800710009_C

value: bevacizumab

value: immunoreactive


title: RNA-Seq_patient_7_primary


title: RNA-Seq_patient_9_omentum


title: X5800701030_G

value: mesenchymal


title: X5800701030_F

value: ovarian cancer

value: IV


title: X5800701019_K

value: FFPE

value: other


title: RNA-Seq_patient_6_omentum


title: RNA-Seq_patient_6_primary


title: RNA-Seq_patient_5_omentum


title: X5800710002_E

value: differentiated


title: RNA-Seq_patient_4_primary


title: X5800710038_D

value: proliferative

value: II


title: X5801106019_J

value: SUB-OPTIMAL


title: RNA-Seq_patient_2_omentum

value: High grade serous ovarian cancer

value: rRNA-depleted RNA


title: RNA-Seq_patient_3_primary

value: primary tumor


title: X5800710002_C

value: standard

value: I


title: X5800710001_K

value: OPTIMAL

value: III

value: serous


title: X5800701019_E


title: RNA-Seq_patient_1_omentum

value: metastatic tumor


title: X5800701029_C

value: ovarian cancer

value: bevacizumab


title: X5800744004_B

value: FFPE

value: immunoreactive


title: X5800701019_D


title: X5800710047_I

value: mesenchymal

value: IV


title: RNA-Seq_patient_1_primary


title: Mouse Kidney M5 +AlkB ARM-seq

city: Santa Cruz

first: Todd

address: 1156 High Street

department: Biomolecular Engineering and Bioinformatics

institute: University of California Santa Cruz

description: total small RNA (≤ 250 nts)

data_processing:
Adapters were removed and reads were merged with SeqPrep [John st. John unpub] using a minimum read length of 15 and adapters AGATCGGAAGAGCACACGTC and GATCGTCGGACTGTAGAACTC.  Reads that could not be merged were discarded before mapping.
Data were analyzed with TRAX (https://github.com/UCSC-LoweLab/tRAX) with fragment counts disabled, TRAX maps reads using bowtie2 to a custom database containing mature tRNA transcripts and the genome sequence.
tRNAs were converted into genome space with TRAX and coverage tracks were created with bedGraphToBigWig and genomeCoverageBed from UCSC Genome Browser tools and BEDtools.
Genome_build: Mus musculus GRCm38/mm10
Supplementary_files_format_and_content: Processed data files are in bigwig format and can be visualized by uploading them into the UCSC Genome Browser. They contain the read coverage aligned to the reference genome.

organism: Mus musculus

source_name: C57BL/6J male mouse Kidney

growth_protocol: Samples were obtained from 3 C57BL/6J male 6-8 weeks old timepoints. Mice are housed in facilities with roughly 12 hr light-dark cycles (7AM-7PM light and 7PM-7AM dark)

extract_protocol:
Isolation of total RNA from mouse Kidney tissue was performed using Direct-Zol RNA MiniPrep Kit (Zymo Research) with TRI Reagent (Molecular Research Center, Inc.), typically yielding 400–450 μg of total RNA. Appropriate amounts of TRI Reagents was added to each tissue sample, along with ~400 uL of zirconium silicate beads (1.0 mm), and samples were homoginized using a tissue homoginization centrifuge. Sample size (n = 3) was selected to demonstrate the utility of the protocol at a level of replication achievable by most researchers.30 μg of control or AlkB-treated RNA were processed using the MirVana miRNA Isolation Kit (Life Technologies), according to the manufacturer's instructions, to select for RNA <200 nt. RNA was concentrated to 30 μg using RNA Clean and Concentrate-25 (Zymo Research), and was treated with DNase I (New England BioLabs). Following column cleanup of the RNA, 800ng was used as input for NEBNext Small RNA Library Prep Kit for Illumina (New England BioLabs).  Total Small RNA was isolated from Total RNA samples from each Kidney tissue sample using the miRvana small RNA isolation protocol (Life Technologies). Small RNA samples were divided and treated as minus AlkB control treatment and plus-AlkB experimental treatment. AlkB treatment was performed as previously described (Cozen et al. Nat Methods. 2015). All samples were then treated with T4PNK at pH 6.5 to maximize 3' phosphatase activity for 30 mins. Finally RNA was concentrated after each enzymatic treatment using an RNA clean and concentration-5 kit (Zymo Research). Treated RNA was used for library preparation.
For ARM-seq, libraries were constructed as previously described (Hrabeta-Robinson, et al. Methods Mol Biol. 2017) which utilizes the NEBNext Multiplex Small RNA Library Prep Set (NEB).  For RNA-seq, and Panc1 RIP-seq,  NEXTflex™ Rapid Directional qRNA-Seq™ For ARM-seq, 30 μg of control or AlkB-treated RNA were processed using the MirVana miRNA Isolation Kit (Life Technologies), according to the manufacturer's instructions, to select for RNA <200 nt. RNA was concentrated to 2ug using RNA Clean and Concentrate-25 (Zymo Research), and was treated with DNase I (New England BioLabs). Following column cleanup of the RNA, 800ng was used as input for NEBNext Small RNA Library Prep Kit for Illumina (New England BioLabs).

treatment_protocol: All samples were collected from said mice at 2-3 PM EST. All tissue samples were then flash-frozen in liquid nitrogen and stored in -80˚C freezer until use.

value: Whole Kidney

tag: Sex

value: male


title: Mouse Kidney M6 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: RNA-Seq_patient_3_omentum

value: High grade serous ovarian cancer


title: RNA-Seq_patient_2_primary

value: rRNA-depleted RNA


title: Mouse Kidney M4 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: Mouse Kidney M6 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: X5800710038_J


title: Mouse Kidney M5 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: Mouse Kidney M4 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: Mouse Liver M5 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)

source_name: C57BL/6J male mouse Liver

extract_protocol:
Isolation of total RNA from mouse Liver tissue was performed using Direct-Zol RNA MiniPrep Kit (Zymo Research) with TRI Reagent (Molecular Research Center, Inc.), typically yielding 400–450 μg of total RNA. Appropriate amounts of TRI Reagents was added to each tissue sample, along with ~400 uL of zirconium silicate beads (1.0 mm), and samples were homoginized using a tissue homoginization centrifuge. Sample size (n = 3) was selected to demonstrate the utility of the protocol at a level of replication achievable by most researchers. 50 μg of control or AlkB-treated RNA were processed using the MirVana miRNA Isolation Kit (Life Technologies), according to the manufacturer's instructions, to select for RNA <200 nt. RNA was concentrated to using a RNA Clean and Concentrate-25 (Zymo Research), after an on-column DNase I treatment to remove residual DNA. (New England BioLabs). Small RNA samples were divided and treated as minus AlkB control treatment and plus-AlkB experimental treatment. AlkB treatment was performed as previously described (Cozen et al. Nat Methods. 2015). Finally, RNA was concentrated after each enzymatic treatment using an RNA clean and concentration-5 kit (Zymo Research). Treated RNA was used for library preparation.                        Total RNA samples were obtained from HCC (control and experimental) mouse liver samples from the Kay lab (Stanford).  Roughly 25-30 ug of total RNA was supplied from a TRIzol RNA isolation.  These samples were then treated as above (starting from MirVana step) to obtain - and + AlkB-treated RNAs for ARM-seq library preparation. All RNA supplied was put through extraction protocol. (Note: DNase I step was ommitted in preparation of these samples)
For ARM-seq, libraries were constructed as previously described (Hrabeta-Robinson, et al. Methods Mol Biol. 2017) which utilizes the NEBNext Multiplex Small RNA Library Prep Set (NEB). PCR-amplified libraries were purified using DNA Clean and Concentrate-5 (Zymo Research) and then size-selected (140-250 nts) on a 6% non-denaturing TBE-acrylamide gel. Libraries were eluted from gel pieces using Gel Elution Buffer (NEB) and precipitated using .3 M NaOAc, 80% Ethanol, and 1 uL of Linear Acrylamide (supplied in NEBNext Kit) at final concentration.  Samples were left in -80C freezer overnight to precipitate. Precipitated libraries were then pelleted, washed twice in 80% Ethanol, and resuspended in Pure H2O. Libraries were then quantified using NanoDrop and Agilent DNA High Sensitivity kit.                                                                                For DM-tRNA-seq, libraries were constructed as using the TGIRT™ Improved Modular Template-Switching RNA-seq Kit (InGex, LLC), which utilizes Illumina-compatible adapters for amplification and sequencing purposes. Libraries were amplified using PCR primers supplied with the NEBNext Small RNA library Prep Set (NEB) and  purified using Agencourt AMPure XP beads (Beckman). Resulting purified sequencing libraries were quantified using NanoDrop and Agilent DNA High Sensitivity kit. Libraries were then pooled equimolarly, and concentrated using a DNA Clean and Concentrate-5 (Zymo Research).  Pooled PCR-amplified libraries were size-selected (140-250 nts) on a 6% non-denaturing TBE-acrylamide gel to remove unwanted primer dimer products. Libraries were eluted from gel pieces using Gel Elution Buffer (NEB) and precipitated using .3 M NaOAc, 80% Ethanol, and 1 uL of Linear Acrylamide (supplied in NEBNext Kit) at final concentration.  Samples were left in -80C freezer overnight to precipitate. Precipitated libraries wer then pelleted, washed twice in 80% Ethanol, and resuspended in Pure H2O.

value: Whole Liver


title: X5800744058_J

value: standard

value: SUB-OPTIMAL


title: Mouse Liver M4 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: Mouse Liver M5 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: X5800710001_C

value: proliferative

value: OPTIMAL

value: other


title: X5800744007_J

value: serous


title: Mouse Thymus M6 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)

source_name: C57BL/6J male mouse Thymus

extract_protocol:
Isolation of total RNA from mouse Thymus tissue was performed using Direct-Zol RNA MiniPrep Kit (Zymo Research) with TRI Reagent (Molecular Research Center, Inc.), typically yielding 400–450 μg of total RNA. Appropriate amounts of TRI Reagents was added to each tissue sample, along with ~400 uL of zirconium silicate beads (1.0 mm), and samples were homoginized using a tissue homoginization centrifuge. Sample size (n = 3) was selected to demonstrate the utility of the protocol at a level of replication achievable by most researchers.30 μg of control or AlkB-treated RNA were processed using the MirVana miRNA Isolation Kit (Life Technologies), according to the manufacturer's instructions, to select for RNA <200 nt. RNA was concentrated to 30 μg using RNA Clean and Concentrate-25 (Zymo Research), and was treated with DNase I (New England BioLabs). Following column cleanup of the RNA, 300ng was used as input for NEBNext Small RNA Library Prep Kit for Illumina (New England BioLabs).  Total Small RNA was isolated from Total RNA samples from each Thymus tissue sample using the miRvana small RNA isolation protocol (Life Technologies). Small RNA samples were divided and treated as minus AlkB control treatment and plus-AlkB experimental treatment. AlkB treatment was performed as previously described (Cozen et al. Nat Methods. 2015). All samples were then treated with T4PNK at pH 6.5 to maximize 3' phosphatase activity for 30 mins. Finally RNA was concentrated after each enzymatic treatment using an RNA clean and concentration-5 kit (Zymo Research). Treated RNA was used for library preparation.
For ARM-seq, libraries were constructed as previously described (Hrabeta-Robinson, et al. Methods Mol Biol. 2017) which utilizes the NEBNext Multiplex Small RNA Library Prep Set (NEB).  For RNA-seq, and Panc1 RIP-seq,  NEXTflex™ Rapid Directional qRNA-Seq™ For ARM-seq, 30 μg of control or AlkB-treated RNA were processed using the MirVana miRNA Isolation Kit (Life Technologies), according to the manufacturer's instructions, to select for RNA <200 nt. RNA was concentrated to 1ug using RNA Clean and Concentrate-25 (Zymo Research), and was treated with DNase I (New England BioLabs). Following column cleanup of the RNA, 300ng was used as input for NEBNext Small RNA Library Prep Kit for Illumina (New England BioLabs).

value: Whole Thymus


title: X5801106023_I

value: ovarian cancer

value: bevacizumab

value: differentiated

value: III


title: Mouse Thymus M5 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: Mouse Thymus M4 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: X5800701029_B

value: FFPE


title: Mouse Thymus M6 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: X5800710038_E

value: IV


title: X5801106023_J


title: X5800744025_G

value: immunoreactive


title: Mouse Thymus M4 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)

value: male


title: X5800710007_J


title: X6828280034_H


title: RNA-Seq_patient_10_omentum

value: High grade serous ovarian cancer

value: metastatic tumor

value: rRNA-depleted RNA


title: HPC-7_HSP90i_Rep2

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
RNA-seq reads were trimmed with TrimGalore (http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/, v0.4.0) and mapped to Gencode (GRCh37, release: 19 or GRCm38, release m4, respectively) annotation using TopHat2 (Kim, Pertea et al. 2013) (v2.0.13) with the options mate- inner-dist, mate-std-dev and library-type (fr- firststrand). The distance between read mates (mate-inner- dist [http://broadinstitute.github.io/picard.] (v1.1.21). After mapping of the RNA-seq reads from all samples, the reads that mapped uniquely to the genome were counted using featureCounts (Liao, Smyth et al. 2014) with the following options: -Q 10 -p -B -C -s 2. The annotations present in the Homo sapiens gtf file from the Ensembl release 75 were used as reference for counting. DESeq2 (Love, Huber et al. 2014) was used for differential expression analysis of all replicates for each condition. Genes with an adjusted P value < 0.01 and absolute log2 fold change more than 1 were defined as significantly affected.
ChIP-seq reads were aligned to the human genome build hg38 or mouse genome mm10, respectively, using Bowtie2 (Langmead and Salzberg 2012). Duplicate and discordant reads were removed. Peak calling was done with MACS2 (model- based analysis of ChIP- Seq) (Zhang, Liu et al. 2008) using "-- keep-dup all", "--nomodel" and "--extsize 200". Gene annotations and transcript start site (TSS) information for human genes were from taken from Gencode annotation release 26 and for mouse genome from Gencode annotation release m4. For visualization, the paired-end reads were extended to fragment size and normalized to total reads aligned (reads per million, rpm) using deeptools2 (Ramirez, Ryan et al. 2016). Profile plots and heatmaps of ChIP-seq signal were generated with deeptools2 (Ramirez, Ryan et al. 2016).
Genome_build: hg38 / mm10
Supplementary_files_format_and_content: Text file with raw RNA-seq read counts in Control and upon HSP90 inhibition per cell type.
Supplementary_files_format_and_content: Text file with HSP90 ChIP-seq peaks in K562 cells.

extract_protocol: RNA isolation was done using TRI-Reagent (Sigma Aldrich, #T9424) according to manufacturer’s.

treatment_protocol: Hsp90 inhibition was carried out using the following concentrations of NVP-AUY922 for 16h hours with the corresponding cell types: 50nM for HPC-7, 200nM for MEFs and 300nM for K562.

tag: cell line

tag: condition

value: HSP90 inhibition


title: X5800744014_J

tag: tissue preparation

value: standard


title: HPC-7_HSP90i_Rep3


title: X5800710002_L

value: proliferative

value: SUB-OPTIMAL

tag: newgrade


title: X5800744036_I

value: OPTIMAL

value: II

value: serous

tag: age


title: HPC-7_HSP90i_Rep1


title: X5801106019_F

value: ovarian cancer

value: bevacizumab

value: mesenchymal

tag: plate


title: X5800710041_C

value: FFPE

value: III


title: X5800710007_D

value: immunoreactive

value: other


title: X5800744014_E


title: HPC-7_Control_Rep3

value: Control


title: Mouse Thymus M5 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)

value: Whole Thymus

value: male


title: X5800744060_F


title: X5800710029_K


title: X5800744019_I


title: HPC-7_Control_Rep2


title: HPC-7_Control_Rep1


title: X5800744019_A

value: differentiated


title: X6828280034_F

value: standard


title: 2%DMSO_rep2

city: Seoul

first: Min-Hee

last: Kang

state: Seoul

address: 120 Neungdong-ro

department: Stem Cell and Regenerative Biotechnology

country: South Korea

institute: Konkuk University

data_processing:
Sequenced reads were pseudomapped onto ENSEMBLE transcript database (mm10) using kallisto and then quantification was performed with tximport to summarize the gene-level abundance (TPM)
For genome coverage, sequenced reads were mapped onto UCSC reference genome (mm10) by STAR to generate bam format. Sorted bam file by samtools was subjected to make genome coverage histogram(bedgraph) using bedtools (bedtools genomcov -ibam -bg -split).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample and bedgraph files contain genome coverage histogram on mm10 of each sample.

source_name: 2-cell embryos_2%DMSO

growth_protocol: Zygotes were cultured with KSOM media at 37℃ incubator with 5% CO2

extract_protocol:
Fifty of 2-cell embryos for each group were collected in 1.5ml tube and then washed with PBS one time. After removing PBS and then the embryos were directly lysed and used for cDNA synthesis.
For cDNA synthesis and amplification with low amount of RNA from embryos, we used SMARTer® Ultra® Low Input RNA Kit (Clonetech, 634940) according to the manufacturer’s instructions. Using Agilent Bioanalyzer High Sensitivity DNA kit (Agilent, 5067-4626), size and quantity of amplified cDNA were estimated in 400-10,000bp and 2-10ng, respectively. Synthesized cDNA (2ng) was sheared into 150-200 bp size by Covaris™ M220 Focused-ultrasonicator™ (Thermo Fisher Scientific, 4482277) then used for preparation of sequencing library using Low Input DNA Library Prep Kit (Clonetech, 634946) according to the manufacturer’s instructions, followed by single end 50 bp sequencing was run on a HiSeq 2500 sequencer (Illumina).
Libraries were sequenced on Illumina HiSeq2500 sequencer to generate 50bp PE reads.

treatment_protocol: Zygotes were cultured in KSOM media supplemented with or without 2% DMSO for 24 hours and then developed 2-cell embryos with or without DMSO were recovered for further analysis.

tag: strain background

value: BDF1*BDF1 F2

tag: genotype/variation

value: wild type

value: preimplantation embryo

tag: developmental stage

value: 2-cell stage

value: 2% DMSO for 24 hours


title: 2%DMSO_rep1


title: X5800710029_B

value: ovarian cancer

value: OPTIMAL

value: serous


title: control_rep2

source_name: 2-cell embryos_control

value: none (control)


title: control_rep1


title: RNA-Seq_patient_4_omentum

value: High grade serous ovarian cancer

value: metastatic tumor

value: rRNA-depleted RNA


title: Mouse Distal Colon M6 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)

source_name: C57BL/6J male mouse Distal Colon

extract_protocol:
Isolation of total RNA from mouse Distal Colon tissue was performed using Direct-Zol RNA MiniPrep Kit (Zymo Research) with TRI Reagent (Molecular Research Center, Inc.), typically yielding 400–450 μg of total RNA. Appropriate amounts of TRI Reagents was added to each tissue sample, along with ~400 uL of zirconium silicate beads (1.0 mm), and samples were homoginized using a tissue homoginization centrifuge. Sample size (n = 3) was selected to demonstrate the utility of the protocol at a level of replication achievable by most researchers.30 μg of control or AlkB-treated RNA were processed using the MirVana miRNA Isolation Kit (Life Technologies), according to the manufacturer's instructions, to select for RNA <200 nt. RNA was concentrated to 30 μg using RNA Clean and Concentrate-25 (Zymo Research), and was treated with DNase I (New England BioLabs). Following column cleanup of the RNA, 700ng was used as input for NEBNext Small RNA Library Prep Kit for Illumina (New England BioLabs).  Total Small RNA was isolated from Total RNA samples from each Distal Colon tissue sample using the miRvana small RNA isolation protocol (Life Technologies). Small RNA samples were divided and treated as minus AlkB control treatment and plus-AlkB experimental treatment. AlkB treatment was performed as previously described (Cozen et al. Nat Methods. 2015). All samples were then treated with T4PNK at pH 6.5 to maximize 3' phosphatase activity for 30 mins. Finally RNA was concentrated after each enzymatic treatment using an RNA clean and concentration-5 kit (Zymo Research). Treated RNA was used for library preparation.
For ARM-seq, libraries were constructed as previously described (Hrabeta-Robinson, et al. Methods Mol Biol. 2017) which utilizes the NEBNext Multiplex Small RNA Library Prep Set (NEB).  For RNA-seq, and Panc1 RIP-seq,  NEXTflex™ Rapid Directional qRNA-Seq™ For ARM-seq, 30 μg of control or AlkB-treated RNA were processed using the MirVana miRNA Isolation Kit (Life Technologies), according to the manufacturer's instructions, to select for RNA <200 nt. RNA was concentrated to 2ug using RNA Clean and Concentrate-25 (Zymo Research), and was treated with DNase I (New England BioLabs). Following column cleanup of the RNA, 700ng was used as input for NEBNext Small RNA Library Prep Kit for Illumina (New England BioLabs).

value: Whole Distal Colon

tag: strain


title: Mouse Distal Colon M5 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Distal Colon M4 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Distal Colon M6 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Distal Colon M5 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Distal Colon M4 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Distal Colon M6 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: X5800710007_A

value: FFPE

value: bevacizumab

value: SUB-OPTIMAL

value: IV


title: X5800710001_L

value: immunoreactive


title: X5801106022_B

value: proliferative

value: III

value: other


title: X5800710038_F

value: standard


title: X5800701057_E

value: ovarian cancer

value: differentiated

value: II


title: X5800701006_G

value: mesenchymal

value: OPTIMAL

value: serous


title: X5800710009_G


title: X5800744041_K


title: Mouse Distal Colon M5 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)

value: male


title: X5800710002_I


title: Mouse Distal Colon M4 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)

value: Whole Distal Colon


title: X5800701019_F

value: FFPE


title: X5800710001_B


title: X5800701019_H

value: bevacizumab

value: I


title: Mouse Distal Colon M6 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: Mouse Distal Colon M5 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: Mouse Distal Colon M4 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: X6828280034_J

value: IV


title: X5800701027_H


title: Mouse Proximal Colon M6 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)

source_name: C57BL/6J male mouse Proximal Colon

extract_protocol:
Isolation of total RNA from mouse Proximal Colon tissue was performed using Direct-Zol RNA MiniPrep Kit (Zymo Research) with TRI Reagent (Molecular Research Center, Inc.), typically yielding 400–450 μg of total RNA. Appropriate amounts of TRI Reagents was added to each tissue sample, along with ~400 uL of zirconium silicate beads (1.0 mm), and samples were homoginized using a tissue homoginization centrifuge. Sample size (n = 3) was selected to demonstrate the utility of the protocol at a level of replication achievable by most researchers.30 μg of control or AlkB-treated RNA were processed using the MirVana miRNA Isolation Kit (Life Technologies), according to the manufacturer's instructions, to select for RNA <200 nt. RNA was concentrated to 30 μg using RNA Clean and Concentrate-25 (Zymo Research), and was treated with DNase I (New England BioLabs). Following column cleanup of the RNA, 700ng was used as input for NEBNext Small RNA Library Prep Kit for Illumina (New England BioLabs).  Total Small RNA was isolated from Total RNA samples from each Proximal Colon tissue sample using the miRvana small RNA isolation protocol (Life Technologies). Small RNA samples were divided and treated as minus AlkB control treatment and plus-AlkB experimental treatment. AlkB treatment was performed as previously described (Cozen et al. Nat Methods. 2015). All samples were then treated with T4PNK at pH 6.5 to maximize 3' phosphatase activity for 30 mins. Finally RNA was concentrated after each enzymatic treatment using an RNA clean and concentration-5 kit (Zymo Research). Treated RNA was used for library preparation.
For ARM-seq, libraries were constructed as previously described (Hrabeta-Robinson, et al. Methods Mol Biol. 2017) which utilizes the NEBNext Multiplex Small RNA Library Prep Set (NEB).  For RNA-seq, and Panc1 RIP-seq,  NEXTflex™ Rapid Directional qRNA-Seq™ For ARM-seq, 30 μg of control or AlkB-treated RNA were processed using the MirVana miRNA Isolation Kit (Life Technologies), according to the manufacturer's instructions, to select for RNA <200 nt. RNA was concentrated to 2ug using RNA Clean and Concentrate-25 (Zymo Research), and was treated with DNase I (New England BioLabs). Following column cleanup of the RNA, 700ng was used as input for NEBNext Small RNA Library Prep Kit for Illumina (New England BioLabs).

value: Whole Proximal Colon


title: X5800701006_D

value: proliferative


title: X5800701057_K


title: X5801106023_F

value: immunoreactive

value: III


title: Mouse Proximal Colon M6 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: X5800701030_J

value: standard

value: SUB-OPTIMAL

value: other


title: X5800710007_B

value: ovarian cancer

value: differentiated


title: Mouse Proximal Colon M4 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Proximal Colon M4 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: X5800744042_D

value: OPTIMAL


title: X5800701057_L

value: mesenchymal

value: serous


title: Mouse Proximal Colon M6 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)

value: male


title: Mouse Proximal Colon M5 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: X5800744040_G

value: FFPE


title: RNA-Seq_patient_5_primary

tag: subject status

value: High grade serous ovarian cancer

value: primary tumor

value: rRNA-depleted RNA


title: Mouse Proximal Colon M5 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)

value: Whole Proximal Colon


title: Mouse Proximal Colon M6 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: Mouse Proximal Colon M5 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: X5800710007_C

value: bevacizumab


title: Mouse Proximal Colon M5 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: X5800744025_E

value: immunoreactive


title: X5800701021_L

value: III


title: Mouse Proximal Colon M4 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: X5801106019_A

value: standard


title: X5800710002_K

value: I


title: Mouse Brain M6 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)

source_name: C57BL/6J male mouse brain

extract_protocol:
Isolation of total RNA from mouse Brain tissue was performed using Direct-Zol RNA MiniPrep Kit (Zymo Research) with TRI Reagent (Molecular Research Center, Inc.), typically yielding 400–450 μg of total RNA. Appropriate amounts of TRI Reagents was added to each tissue sample, along with ~400 uL of zirconium silicate beads (1.0 mm), and samples were homoginized using a tissue homoginization centrifuge. Sample size (n = 3) was selected to demonstrate the utility of the protocol at a level of replication achievable by most researchers.50 μg of control or AlkB-treated RNA were processed using the MirVana miRNA Isolation Kit (Life Technologies), according to the manufacturer's instructions, to select for RNA <200 nt. RNA was concentrated to using a RNA Clean and Concentrate-25 (Zymo Research), after an on-column DNase I treatment to remove residual DNA. (New England BioLabs). Small RNA samples were divided and treated as minus AlkB control treatment and plus-AlkB experimental treatment. AlkB treatment was performed as previously described (Cozen et al. Nat Methods. 2015). All samples were then treated with T4PNK at pH 6.5 (to maximize 3' phosphatase activity) for 30 mins. Finally, RNA was concentrated after each enzymatic treatment using an RNA clean and concentration-5 kit (Zymo Research). Treated RNA was used for library preparation.
For ARM-seq, libraries were constructed as previously described (Hrabeta-Robinson, et al. Methods Mol Biol. 2017) which utilizes the NEBNext Multiplex Small RNA Library Prep Set (NEB). PCR-amplified libraries were purified using DNA Clean and Concentrate-5 (Zymo Research) and then size-selected (140-250 nts) on a 6% non-denaturing TBE-acrylamide gel. Libraries were eluted from gel pieces using Gel Elution Buffer (NEB) and precipitated using .3 M NaOAc, 80% Ethanol, and 1 uL of Linear Acrylamide (supplied in NEBNext Kit) at final concentration.  Samples were left in -80C freezer overnight to precipitate. Precipitated libraries were then pelleted, washed twice in 80% Ethanol, and resuspended in Pure H2O. Libraries were then quantified using NanoDrop and Agilent DNA High Sensitivity kit.                                                                                For DM-tRNA-seq, libraries were constructed as using the TGIRT™ Improved Modular Template-Switching RNA-seq Kit (InGex, LLC), which utilizes Illumina-compatible adapters for amplification and sequencing purposes. Libraries were amplified using PCR primers supplied with the NEBNext Small RNA library Prep Set (NEB) and  purified using Agencourt AMPure XP beads (Beckman). Resulting purified sequencing libraries were quantified using NanoDrop and Agilent DNA High Sensitivity kit. Libraries were then pooled equimolarly, and concentrated using a DNA Clean and Concentrate-5 (Zymo Research).  Pooled PCR-amplified libraries were size-selected (140-250 nts) on a 6% non-denaturing TBE-acrylamide gel to remove unwanted primer dimer products. Libraries were eluted from gel pieces using Gel Elution Buffer (NEB) and precipitated using .3 M NaOAc, 80% Ethanol, and 1 uL of Linear Acrylamide (supplied in NEBNext Kit) at final concentration.  Samples were left in -80C freezer overnight to precipitate. Precipitated libraries wer then pelleted, washed twice in 80% Ethanol, and resuspended in Pure H2O.

value: Whole Brain


title: X5800710002_H

source_name: FFPE Ovarian Cancer

value: ovarian cancer

value: other


title: Mouse Brain M5 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: X5800710001_F

value: differentiated

value: OPTIMAL


title: X5800710001_G

value: II

value: serous


title: Mouse Brain M4 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)

value: male


title: Mouse Brain M6 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Proximal Colon M4 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: X5800744036_G

value: FFPE

value: IV


title: Mouse Brain M4 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: X5800710008_L

value: proliferative


title: Mouse Brain M5 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Brain M5 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: Mouse Brain M6 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: Mouse Brain M4 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: Mouse Brain M5 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: X5800710038_I


title: X5800710001_I

value: mesenchymal


title: X5801106022_H

value: SUB-OPTIMAL


title: X5800701057_J

value: immunoreactive


title: X5800744019_H

value: bevacizumab


title: X5800744007_A

value: III


title: Mouse Heart M6 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)

source_name: C57BL/6J male mouse Heart

extract_protocol:
Isolation of total RNA from mouse Heart tissue was performed using Direct-Zol RNA MiniPrep Kit (Zymo Research) with TRI Reagent (Molecular Research Center, Inc.), typically yielding 400–450 μg of total RNA. Appropriate amounts of TRI Reagents was added to each tissue sample, along with ~400 uL of zirconium silicate beads (1.0 mm), and samples were homoginized using a tissue homoginization centrifuge. Sample size (n = 3) was selected to demonstrate the utility of the protocol at a level of replication achievable by most researchers.50 μg of control or AlkB-treated RNA were processed using the MirVana miRNA Isolation Kit (Life Technologies), according to the manufacturer's instructions, to select for RNA <200 nt. RNA was concentrated to using a RNA Clean and Concentrate-25 (Zymo Research), after an on-column DNase I treatment to remove residual DNA. (New England BioLabs). Small RNA samples were divided and treated as minus AlkB control treatment and plus-AlkB experimental treatment. AlkB treatment was performed as previously described (Cozen et al. Nat Methods. 2015).  Finally, RNA was concentrated after each enzymatic treatment using an RNA clean and concentration-5 kit (Zymo Research). Treated RNA was used for library preparation.
For ARM-seq, libraries were constructed as previously described (Hrabeta-Robinson, et al. Methods Mol Biol. 2017) which utilizes the NEBNext Multiplex Small RNA Library Prep Set (NEB). PCR-amplified libraries were purified using DNA Clean and Concentrate-5 (Zymo Research) and then size-selected (140-250 nts) on a 6% non-denaturing TBE-acrylamide gel. Libraries were eluted from gel pieces using Gel Elution Buffer (NEB) and precipitated using .3 M NaOAc, 80% Ethanol, and 1 uL of Linear Acrylamide (supplied in NEBNext Kit) at final concentration.  Samples were left in -80C freezer overnight to precipitate. Precipitated libraries were then pelleted, washed twice in 80% Ethanol, and resuspended in Pure H2O. Libraries were then quantified using NanoDrop and Agilent DNA High Sensitivity kit.                                                                                For DM-tRNA-seq, libraries were constructed as using the TGIRT™ Improved Modular Template-Switching RNA-seq Kit (InGex, LLC), which utilizes Illumina-compatible adapters for amplification and sequencing purposes. Libraries were amplified using PCR primers supplied with the NEBNext Small RNA library Prep Set (NEB) and  purified using Agencourt AMPure XP beads (Beckman). Resulting purified sequencing libraries were quantified using NanoDrop and Agilent DNA High Sensitivity kit. Libraries were then pooled equimolarly, and concentrated using a DNA Clean and Concentrate-5 (Zymo Research).  Pooled PCR-amplified libraries were size-selected (140-250 nts) on a 6% non-denaturing TBE-acrylamide gel to remove unwanted primer dimer products. Libraries were eluted from gel pieces using Gel Elution Buffer (NEB) and precipitated using .3 M NaOAc, 80% Ethanol, and 1 uL of Linear Acrylamide (supplied in NEBNext Kit) at final concentration.  Samples were left in -80C freezer overnight to precipitate. Precipitated libraries wer then pelleted, washed twice in 80% Ethanol, and resuspended in Pure H2O.

value: Whole Heart


title: X5800710029_G

value: standard


title: Mouse Heart M4 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Brain M4 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)

value: Whole Brain


title: Mouse Heart M5 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Heart M6 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Heart M5 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Brain M6 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: X5801106023_C

value: ovarian cancer


title: X5800744060_G


title: Mouse Liver M4 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)

value: Whole Liver


title: X5801106022_F

value: OPTIMAL


title: X5800701029_G


title: X5800744060_D

value: differentiated

value: II


title: X5801106023_D

value: serous


title: X5800744040_L

value: FFPE


title: Mouse Liver M6 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)

value: male


title: X5800710052_D

value: proliferative


title: X5800701006_C

value: IV


title: Mouse Liver M4 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Liver M4 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Liver M6 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Heart M4 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Liver M5 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Spleen M5 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)

source_name: C57BL/6J male mouse Spleen

extract_protocol:
Isolation of total RNA from mouse Spleen tissue was performed using Direct-Zol RNA MiniPrep Kit (Zymo Research) with TRI Reagent (Molecular Research Center, Inc.), typically yielding 400–450 μg of total RNA. Appropriate amounts of TRI Reagents was added to each tissue sample, along with ~400 uL of zirconium silicate beads (1.0 mm), and samples were homoginized using a tissue homoginization centrifuge. Sample size (n = 3) was selected to demonstrate the utility of the protocol at a level of replication achievable by most researchers.30 μg of control or AlkB-treated RNA were processed using the MirVana miRNA Isolation Kit (Life Technologies), according to the manufacturer's instructions, to select for RNA <200 nt. RNA was concentrated to 30 μg using RNA Clean and Concentrate-25 (Zymo Research), and was treated with DNase I (New England BioLabs). Following column cleanup of the RNA, 700ng was used as input for NEBNext Small RNA Library Prep Kit for Illumina (New England BioLabs).  Total Small RNA was isolated from Total RNA samples from each Spleen tissue sample using the miRvana small RNA isolation protocol (Life Technologies). Small RNA samples were divided and treated as minus AlkB control treatment and plus-AlkB experimental treatment. AlkB treatment was performed as previously described (Cozen et al. Nat Methods. 2015). All samples were then treated with T4PNK at pH 6.5 to maximize 3' phosphatase activity for 30 mins. Finally RNA was concentrated after each enzymatic treatment using an RNA clean and concentration-5 kit (Zymo Research). Treated RNA was used for library preparation.
For ARM-seq, libraries were constructed as previously described (Hrabeta-Robinson, et al. Methods Mol Biol. 2017) which utilizes the NEBNext Multiplex Small RNA Library Prep Set (NEB).  For RNA-seq, and Panc1 RIP-seq,  NEXTflex™ Rapid Directional qRNA-Seq™ For ARM-seq, 30 μg of control or AlkB-treated RNA were processed using the MirVana miRNA Isolation Kit (Life Technologies), according to the manufacturer's instructions, to select for RNA <200 nt. RNA was concentrated to 2ug using RNA Clean and Concentrate-25 (Zymo Research), and was treated with DNase I (New England BioLabs). Following column cleanup of the RNA, 700ng was used as input for NEBNext Small RNA Library Prep Kit for Illumina (New England BioLabs).

value: Whole Spleen


title: Mouse Spleen M6 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Spleen M6 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Spleen M5 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Spleen M4 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Spleen M6 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: Mouse Spleen M4 -AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: Mouse Liver M5 +AlkB DM-tRNA-seq

description: total small RNA (≤ 250 nts)


title: X5800701010_F

value: immunoreactive

value: other


title: X5800710016_G

value: III


title: X5800710009_A

value: bevacizumab

value: mesenchymal


title: Mouse Spleen M5 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: Mouse Spleen M4 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: Mouse Spleen M5 +AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: X5800710041_I

value: standard


title: Mouse Spleen M4 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: X5800701055_I

value: ovarian cancer


title: X5800710038_H

value: SUB-OPTIMAL


title: Mouse Spleen M6 -AlkB ARM-seq

description: total small RNA (≤ 250 nts)


title: MEF_HSP90i_Rep2

source_name: MEF

value: MEF

value: HSP90 inhibition


title: MEF_HSP90i_Rep3


title: X5800744025_H

value: OPTIMAL


title: X5800701029_J

value: serous


title: X5800701029_I

value: FFPE


title: X5800701029_D


title: MEF_HSP90i_Rep1


title: X5800701057_C


title: X5800701027_D

value: differentiated


title: MEF_Control_Rep3

value: Control


title: X5800701027_G


title: X5800710029_F

value: proliferative

value: II


title: X5800701027_A

value: IV


title: X5800710038_B


title: X5800701010_C


title: MEF_Control_Rep1


title: cd71_cb2_ag221

city: Palo Alto

first: Ritika

last: Dutta

address: 265 Campus Drive

institute: Stanford School of Medicine

description:
Markers sorted on: CD34+ enriched cells sorted on CD71+ marker after 6 days in erythroid differentiation media.
Time in culture: After sorting, cultured for 24 hours with AG221 (Enasidenib) 10uM in StemSpan + Erythroid Expansion Supplement.
processed data file: Raw_Read_Counts.csv

data_processing:
cDNA libraries were sequenced on the Illumina Nextseq platform to obtain 80-bp single-end reads. The reads were trimmed, 2 nt on each end, to remove low quality parts, and improve mapping to the genome. The 78 nt reads that resulted were compressed by removing duplicates, but keeping track of how many times each sequence occurred in each sample in a database. (Performed by Girihlet)
The unique reads were then mapped to the human genome, using exact matches. Each mapped read was then assigned annotations from the underlying genome. In case of multiple annotations (e.g. a miRNA occurring in the intron of a gene), a hierarchy based on heuristics was used to give a unique identity to each read. This was then used to identify the reads belonging to each transcript and coverage over each position on the transcript was established. Median of this coverage was used as an estimate of the gene's expression value. (Performed by Girihlet)
The raw read count matrix was normalized and differentiation expression was determined using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Raw_Read_Counts.numbers.csv: Comma-separated text file with raw read counts.

source_name: Umbilical cord blood

growth_protocol: Cultured enriched CD34+ cells from UCB for 6 days in StemSpan II with 1x Erythroid Expansion Supplement, sorted on CD71+ cells, and then treated with AG221 (Enasidenib) or DMSO for 24 hours in StemSpan II with 1x Erythroid Expansion Supplement.

extract_protocol:
Qiagen RNeasy Kit.
cDNA libraries were prepared using 500ng of total RNA using the TruSeq RNA Sample Preparation Kit v2 (Illumina) - performed by Girihlet.

treatment_protocol: AG221 (Enasidenib) 10uM or DMSO for 24 hours.

tag: cell type

value: CD34+ enriched cells from UCB sorted on CD71+ marker after 6 days in erythroid differentiation media

value: Enasidenib


title: cd71_cb3_ag221


title: cd71_cb3_dmso

description:
Markers sorted on: CD34+ enriched cells sorted on CD71+ marker after 6 days in erythroid differentiation media.
Time in culture: After sorting, cultured for 24 hours with DMSO in StemSpan + Erythroid Expansion Supplement.
processed data file: Raw_Read_Counts.csv

value: DMSO


title: cd71_cb2_dmso


title: cd71_dmso


title: X5800710009_B

extract_protocol: Using FFPE tumor, three 1mm cores were obtained from areas containing >70% tumor nuclei. Total RNA was isolated from these cores using a Qiagen AllPrep DNA/RNA FFPE kit according to the manufacturer's protocol using a Qiacube robot

value: bevacizumab

value: I


title: X5800710007_I

value: ovarian cancer

value: immunoreactive


title: MEF_Control_Rep2

value: MEF


title: X5800701057_G

value: III

value: other


title: X5800701055_H

value: SUB-OPTIMAL

value: serous


title: DoxTam_rep2 ChIP-seq

city: Oslo

first: Shixiong

address: Gaustadalléen 21

department: Centre for Molecular Medicine Norway

country: Norway

institute: University of Oslo

data_processing:
Basecalling with Illumina 1.9 software
FastX Toolkit (0.013) was used to filter out low quality reads, (min. 97% of bases should have quality score of 10). Command: fastq_quality_filter -v -q 10 -p 97 -i  input file -o output file
Quality filtered data was aligned to hg19 assembly with Bowtie 1.1.2. v=2, m=3, k=1.
samtools (1.3.1) was used to convert sam files to bam files, and to remove duplicate in bam files
peaks were called with macs2 (2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include genomic coordinates of PAX2 (HA) peaks called in different treatments

source_name: Mamary gland epithelial cell

growth_protocol: MCF-7 cells were cultured in DMEM with 5% FBS

extract_protocol:
MCF-7 chromatin was sonicated and PAX2 bond genomic regions were isolated by using HA tag antibody.
Libraries were prepared by Norwegian sequencing centre and CRUK genomics core facility

treatment_protocol: Cells were treated with doxycycline (50ng/ml) to induce PAX2 oeverexpresson, followed by tamoxifen (1uM) treatment for 6 hours.

value: Breast adenocarcinoma

tag: gender

value: Female

tag: chip antibody

value: HA tag (abcam:ab9110)

tag: agent

value: doxycycline+ tamoxifen


title: Veh

value: Veh


title: X5800710016_F

tag: tissue

value: FFPE

tag: treatment

value: standard

value: proliferative

value: OPTIMAL


title: cd71_ag221

value: CD34+ enriched cells from UCB sorted on CD71+ marker after 6 days in erythroid differentiation media

value: Enasidenib


title: Dox_rep2 ChIP-seq

tag: cell line

value: doxycycline


title: X6828280001_J

value: ovarian cancer

value: bevacizumab

value: immunoreactive


title: X5800710001_A

value: III


title: X5800701021_F

value: IV

value: serous


title: X5800701056_C

value: II


title: X5800701057_D

value: differentiated


title: X5800710002_J

value: SUB-OPTIMAL


title: X5800701056_D


title: X5800744060_J

value: I

value: other


title: X5800701027_J

value: FFPE

value: standard


title: Sample01_baso0707

city: Baltimore

first: Donald

middle: Welton

last: MacGlashan

state: MD

address: 5501 Hopkins Bayview Circle

department: Allergy and Clinical Immunology

institute: Johns Hopkins University

data_processing:
Bowtie2 (2.2.5)->Samtools (0.1.19) -> peak calling with MACS2 using the hg19 human genome build and HOMER for annotation
Genome_build: hg19

source_name: human basophils

growth_protocol: human peripheral blood->Percoll gradients->negative and positive selection of basophis or B-cels; CD34+ progenitors cultured for 17 days with G1=IL-3 at 5 ng/ml or G3= IL-3/SCF/Flt3L at 5/4/8 ng/ml

extract_protocol: Nextera kit for ATACseq

treatment_protocol: no treatments after harvesting

value: basophil


title: Sample04_Bcell0630

source_name: human B cells

value: B cell


title: X5800701010_D

value: OPTIMAL


title: X5800710009_F

value: mesenchymal


title: X5800710007_H

value: ovarian cancer


title: X5800710001_E

value: bevacizumab


title: Sample09_CD34G3_1213

data_processing:
Bowtie2 (2.2.5)->Samtools (0.1.19) -> peak calling with MACS2 using the hg19 human genome build and HOMER for annotation
Genome_build: hg19
Supplementary_files_format_and_content: peak

source_name: human CD34-derived basophils G3 growth culture


title: Sample07_CD34G3_1204

value: CD34-derived basophils G3 growth culture


title: Sample08_CD34G1_1213

source_name: human CD34-derived basophils G1 growth culture


title: X5800744025_D


title: Sample03_baso0519

value: basophils


title: Sample05_Bcell0525

value: B cells


title: X5800710052_B

value: immunoreactive

value: III

value: serous


title: X5800701057_H

value: proliferative


title: X5800744004_I

value: SUB-OPTIMAL


title: X5800701056_B


title: X5800701057_I


title: X5800710002_F


title: X5800744019_B


title: Sample02_baso1128


title: PRO-seq ∆264 rep1

description:
1402-AW-3-CAGATC_S3
processed data file: PROseq_pp_gb.count.txt

data_processing:
Library strategy: PRO-seq
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Reads with mapping quality less than 10 were removed.
Peaks were called by MACS2.
Differential binding peaks were identified using DiffBind based on consensus peaks occurring at least two samples.
After adapter trimming and low quality sequence removal by cutadapt, PRO-seq reads longer than 15bp were reversed complemented using FastX tools.
Reverse complements of the trimmed reads were aligned to the human genome hg19 using Bowtie2.
Reads mapped to rRNA loci and reads with mapping quality less than 10 were removed.
Bam files were given to NRSA (http://bioinfo.vanderbilt.edu/NRSA/) to estimate RNA polymerase abundance in proximal-promoter and gene body regions of genes, to calculate pausing index and pausing index alterations, and to detect enhancers and quantify eRNA changes.
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content:
ChIP-seq: one peak file per Sample
PRO-seq: text file with raw counts for promoter-proximal and gene body region, and density for gene body (ppc, gbc, gbd)
RNA-seq: tab-delimited text file include raw counts for each Sample

source_name: PRO-seq ∆264

extract_protocol:
Chromatin was clarified from sonicated cells and protein-DNA complexes were isolated with antibody.
ChIP libraries were prepared according to New England Biolabs  instructions accompanying the NEBNext Ultar II DNA Library Prep Kit for Illumina (Part# E7645S). After adapter ligation DNA was PCR amplified with NEBNext Multiplex Oligos for Illumina (Part# E7335S and E7500S) for 16 cycles (HA ChIP) or 15 cycles (WDR5 ChIP). For RNA-seq, libraries  were prepared using Poly-A selected at Genewiz using their standard methods, and for PRO-Seq, libraries were made using RNA that was made through a biotin-run on reaction.Biotin-RNA was base hydrolyzed, and extracted. 3'-adaptors were ligated to ends and 5'caps were removed, repaired, and then 5'-adaptors were ligated as well. Purified and intact biotin-RNA containing adaptors was used in a reverase transcriptase reaction to generate cDNA and cDNA was used to amplify full library using NEB High Fidelity Phusion polymerase.RNA libraries were prepared using Poly-A selected RNA.

value: Ramos

value: Burkitt's lymphoma cell line

value: Myc {delta}264-HA

value: 20 nM 4-OHT for 24 hours

tag: molecule subtype

value: nuclear RNA


title: PRO-seq WT rep1

description:
1402-AW-1-CGATGT_S1
processed data file: PROseq_pp_gb.count.txt

source_name: PRO-seq WT

value: Myc WT-HA


title: PRO-seq WBM rep2

description:
1402-AW-5-ATTGGC_S2
processed data file: PROseq_pp_gb.count.txt

source_name: PRO-seq WBM

value: Myc WBM-HA


title: PRO-seq ∆264 rep2

description:
1402-AW-6-CAGATC_S3
processed data file: PROseq_pp_gb.count.txt


title: PRO-seq WBM rep1

description:
1402-AW-2-ATTGGC_S2
processed data file: PROseq_pp_gb.count.txt


title: ChIP-seq WBM-WDR5 rep1

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Reads with mapping quality less than 10 were removed.
Peaks were called by MACS2.
Differential binding peaks were identified using DiffBind based on consensus peaks occurring at least two samples.
After adapter trimming and low quality sequence removal by cutadapt, PRO-seq reads longer than 15bp were reversed complemented using FastX tools.
Reverse complements of the trimmed reads were aligned to the human genome hg19 using Bowtie2.
Reads mapped to rRNA loci and reads with mapping quality less than 10 were removed.
Bam files were given to NRSA (http://bioinfo.vanderbilt.edu/NRSA/) to estimate RNA polymerase abundance in proximal-promoter and gene body regions of genes, to calculate pausing index and pausing index alterations, and to detect enhancers and quantify eRNA changes.
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content:
ChIP-seq: one peak file per Sample
PRO-seq: text file with raw counts for promoter-proximal and gene body region, and density for gene body (ppc, gbc, gbd)
RNA-seq: tab-delimited text file include raw counts for each Sample

source_name: ChIP-seq WBM-WDR5

value: WDR5 (D9E1I from Cell Signaling)


title: ChIP-seq WBM-WDR5 rep3


title: Sample06_CD34G1_1204

value: CD34-derived basophils G1 growth culture


title: PRO-seq WT rep2

description:
1402-AW-4-CGATGT_S1
processed data file: PROseq_pp_gb.count.txt


title: X5800710007_F

value: ovarian cancer

tag: tissue preparation

value: FFPE

value: bevacizumab

value: OPTIMAL


title: X5800744004_C

value: standard

value: IV

tag: newgrade


title: X5800701010_A

value: proliferative

value: III

value: serous

tag: age


title: X5800710016_D

value: immunoreactive

tag: plate


title: X5801106022_C

value: differentiated

value: I

value: other


title: X5800710016_C

value: SUB-OPTIMAL


title: X5801106022_A


title: X5800701027_L


title: X5800701056_J

value: II


title: ChIP-seq WBM-IgG rep3

source_name: ChIP-seq WBM-IgG

value: Ramos

value: Burkitt's lymphoma cell line

value: Myc WBM-HA

value: 20 nM 4-OHT for 24 hours

value: Normal IgG (Cell Signaling)


title: ChIP-seq WBM-IgG rep2


title: X5800701055_F

value: ovarian cancer

value: FFPE

value: mesenchymal

value: OPTIMAL


title: ChIP-seq WBM-IgG rep1


title: ChIP-seq WT-WDR5 rep1

source_name: ChIP-seq WT-WDR5

value: Myc WT-HA

value: WDR5 (D9E1I from Cell Signaling)


title: ChIP-seq WT-WDR5 rep2


title: ChIP-seq WT-IgG rep2

source_name: ChIP-seq WT-IgG


title: X5800710001_J

source_name: FFPE Ovarian Cancer

value: bevacizumab

value: III

value: serous


title: ChIP-seq WT-IgG rep3


title: X5800710009_L

value: immunoreactive


title: X5800710007_E

value: standard

value: proliferative


title: ChIP-seq WT-IgG rep1

value: Ramos


title: X5800710007_G

value: other


title: X5800710002_D

value: I


title: ChIP-seq HA-∆264-1E9-MYC rep2

source_name: ChIP-seq HA-∆264-1E9-MYC

value: Burkitt's lymphoma cell line

value: Myc {delta}264-HA

value: 20 nM 4-OHT for 24 hours

value: HA (C29F4 from Cell Signaling)


title: ChIP-seq WT-WDR5 rep3


title: ChIP-seq WBM-WDR5 rep2

value: Myc WBM-HA


title: X5800701056_G

value: ovarian cancer

value: FFPE

value: SUB-OPTIMAL

value: IV


title: X5800701021_E

value: OPTIMAL

value: II


title: X5800701056_F

value: bevacizumab

value: differentiated

value: III

value: serous


title: X5800710052_C

value: immunoreactive


title: ChIP-seq HA-WBM-1D2-MYC rep2

source_name: ChIP-seq HA-WBM-1D2-MYC

value: Ramos


title: X5800710002_A

value: proliferative


title: X5800701006_E

value: mesenchymal


title: X5800701006_F

value: standard


title: X5800701021_H

value: I


title: X5800701006_K


title: X6828280001_D


title: ChIP-seq HA-WT-5G12 control rep3

source_name: ChIP-seq HA-WT-5G12 control

value: Burkitt's lymphoma cell line

value: 20 nM 4-OHT for 24 hours

value: HA (C29F4 from Cell Signaling)


title: X5800744042_A

value: ovarian cancer

value: FFPE

value: other


title: ChIP-seq HA-WT-3E7-MYC rep1

source_name: ChIP-seq HA-WT-3E7-MYC

value: Myc WT-HA


title: ChIP-seq HA-WT-5G12 control rep1

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Reads with mapping quality less than 10 were removed.
Peaks were called by MACS2.
Differential binding peaks were identified using DiffBind based on consensus peaks occurring at least two samples.
After adapter trimming and low quality sequence removal by cutadapt, PRO-seq reads longer than 15bp were reversed complemented using FastX tools.
Reverse complements of the trimmed reads were aligned to the human genome hg19 using Bowtie2.
Reads mapped to rRNA loci and reads with mapping quality less than 10 were removed.
Bam files were given to NRSA (http://bioinfo.vanderbilt.edu/NRSA/) to estimate RNA polymerase abundance in proximal-promoter and gene body regions of genes, to calculate pausing index and pausing index alterations, and to detect enhancers and quantify eRNA changes.
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content:
ChIP-seq: one peak file per Sample
PRO-seq: text file with raw counts for promoter-proximal and gene body region, and density for gene body (ppc, gbc, gbd)
RNA-seq: text file with raw counts for each Sample


title: ChIP-seq HA-WT-3E7-MYC rep2


title: K562_HSP90i_Rep3

tag: condition

value: HSP90 inhibition


title: ChIP-seq HA-WT-5G12 control rep2

tag: genotype/variation


title: X5800744058_L

value: bevacizumab

value: SUB-OPTIMAL


title: ChIP-seq HA-∆264-1E9-MYC rep3

value: Myc {delta}264-HA


title: ChIP-seq HA-WBM-1D2-MYC rep1

value: Myc WBM-HA


title: ChIP-seq HA-∆264-1E9-MYC rep1

value: Ramos


title: ChIP-seq HA-WBM-1D2-MYC rep3


title: ChIP-seq HA-WT-3E7-MYC rep3


title: K562_HSP90i_Rep1


title: X5800744005_B

value: immunoreactive

value: OPTIMAL


title: K562_Control_Rep3

value: Control


title: X5800710052_I

value: III

value: serous


title: X5800710041_F

value: standard

value: proliferative


title: X5800701056_K

value: ovarian cancer


title: K562_Control_Rep2


title: X5800710009_D

value: FFPE


title: X5800710041_E

value: I


title: miRNA-seq control3

city: Guangzhou

first: Li

last: Chen

address: No. 58, Zhongshan 2nd Road

institute: The First Affiliated Hospital of Sun Yat-sen University

description: miRNA.All.Counts.exp.txt

data_processing:
RNA-seq: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
RNA-seq: Hisat2 2.0.4 mapping to reference genome
miRNA-seq: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) a)10% base quality <15 b) 13% base quality <20 c) 15bp < read length < 30bp.
miRNA-seq: Utilizing the BWA software, we mapped the clean data to miRBase 22.0 Homo Sapiens miRNA database and GRCH38.p10 genome.
Genome_build: GRCh38 / miRBase 22.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: papillary thyroid cancer cells

extract_protocol:
miRNA-seq: Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
RNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols
miRNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TPC-1 cells were cocultured with or without PMN-MDSCs for 48h.

value: untreated


title: miRNA-seq control4

description: miRNA.All.Counts.exp.txt


title: miRNA-seq control2

description: miRNA.All.Counts.exp.txt


title: miRNA-seq coculture6

description: miRNA.All.Counts.exp.txt

value: cocultured with PMN-MDSCs


title: miRNA-seq coculture5

description: miRNA.All.Counts.exp.txt


title: miRNA-seq coculture4

description: miRNA.All.Counts.exp.txt


title: X5800710041_D

data_processing: Illumina Genome Studio for raw vaules.  R for normalized values.

value: mesenchymal

value: IV


title: X5800710016_J

value: SUB-OPTIMAL


title: miRNA-seq coculture3

description: miRNA.All.Counts.exp.txt


title: X5800701057_B

value: other


title: X5800701056_I

value: bevacizumab


title: X5800710047_C

value: immunoreactive


title: X5800701006_B

value: differentiated

value: OPTIMAL


title: K562_Control_Rep1

value: Control


title: miRNA-seq coculture1

description: miRNA.All.Counts.exp.txt


title: X5800744014_K

value: III

value: serous


title: RNA-seq control4

description: all.counts.exp.txt


title: miRNA-seq coculture2

description: miRNA.All.Counts.exp.txt


title: X5800710038_L


title: miRNA-seq control1

description: miRNA.All.Counts.exp.txt


title: X5800701021_D


title: X5800701056_L

value: standard

value: proliferative


title: X5800710008_J

value: ovarian cancer

value: FFPE

value: II


title: X5800744058_G


title: RNA-seq control1

description: all.counts.exp.txt

value: untreated


title: X5800710009_K

value: mesenchymal


title: X5800744007_H


title: X5800701021_K

value: IV


title: RNA-seq coculture6

description: all.counts.exp.txt

value: cocultured with PMN-MDSCs


title: Sample10_CD34G3_0102

value: CD34-derived basophils G3 growth culture


title: X5800710001_D

value: bevacizumab


title: RNA-seq coculture5

description: all.counts.exp.txt


title: RNA-seq coculture4

description: all.counts.exp.txt


title: X5800701021_A

value: immunoreactive


title: X5800701021_I

value: SUB-OPTIMAL

value: other


title: X5800710029_J


title: RNA-seq coculture3

description: all.counts.exp.txt


title: RNA-seq control3

description: all.counts.exp.txt


title: RNA-seq coculture2

description: all.counts.exp.txt


title: RNA-seq coculture1

description: all.counts.exp.txt


title: X5800701006_I

value: OPTIMAL


title: ALL50_Dex rep3_RNA-seq

city: UNSW Sydney

first: Yizhou

description: RNA-seq of ALL50 Dex-treated #3

data_processing:
Raw sequencing reads filtered for adapter contamination, low quality scores, and excluded reads in which more than 10% of bases were unknown.
Filtered paired-end RNA-seq reads aligned to the human genome (hg19) using the software package STAR with standard parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for visualization on the UCSC genome browser

source_name: ALL xenograft cells

extract_protocol:
Cell suspensions of spleens were prepared and mononuclear cells enriched to >97% human by density gradient centrifugation. The spleen-harvested cells were used for ChIP-seq assay. Lysates were clarified from sonicated nuclei and crosslinked protein-DNA complexes were isolated with antibody. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared by Novogene (Hong Kong) for sequencing using standard Illumina protocols

value: ALL xenograft cells

value: Dex

tag: type

value: Resistant


title: ALL50_Dex rep2_RNA-seq

description: RNA-seq of ALL50 Dex-treated #2


title: X5800701055_G

value: differentiated

value: III

value: serous


title: X5800701055_D

value: ovarian cancer

value: FFPE

value: standard

value: proliferative


title: X5800701055_C

value: mesenchymal


title: ALL50_Dex rep1_RNA-seq

description: RNA-seq of ALL50 Dex-treated #1


title: X5800701055_J


title: ALL50_Ctrl rep2_RNA-seq

description: RNA-seq of ALL50 Control #2

value: vehicle


title: ALL50_Ctrl rep1_RNA-seq

description: RNA-seq of ALL50 Control #1


title: ALL54_Dex rep3_RNA-seq

description: RNA-seq of ALL54 Dex-treated #3

value: Sensitive


title: X5800701055_K

value: immunoreactive


title: Expt 2 - CD34(B)-D17(G3 culture method)

description:
the sample title describes a preparation of cells (Expt xx) and the conditions of treatment and follow naming consistent with the published report
mRNA & miRNA

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: GCOS 4.0, the normalized and non-normalized data are the same

source_name: culture

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: 2 forms of preparation: CD34+ cells were cultured in StemPro+supplement+ G1=IL-3(5ng/ml) or G3=IL-3/SCF/Flt3L(5,4,8 ng/ml)

extract_protocol: mRNA was isolated by miRNEasy kit extractions and contained both mRNA and miRNA, RIN values > 6 (lower allowed because of presence of miRNA)

treatment_protocol: no treatments were performed, cells in their resting state after preparation

value: cultured CD34+ cells


title: X5800701055_B

value: SUB-OPTIMAL

value: IV


title: X5800701055_A

value: OPTIMAL


title: ALL50_Ctrl rep3_RNA-seq

description: RNA-seq of ALL50 Control #3

value: ALL xenograft cells


title: Expt 9 - DonorE-pDC

data_processing: due to the way data was processed in the published description of these results (no global normalization), the matrix of results that is normally entered as normalized is not normalized but instead a replicate of the non-normalized data

source_name: peripheral blood

growth_protocol: 2 forms of preparation: CD34+ cells were cultured in StemPro+supplement or basophils, eosinophils and plasmacytoid dendritic cells were purified from the same donor, same blood draw

value: pDendritic Cells:purified to average of 99%


title: ALL54_Dex rep1_RNA-seq

description: RNA-seq of ALL54 Dex-treated #1

value: Dex


title: Expt 9 - DonorE-basophil

value: basophils:purified to average of 99%


title: Expt 2 - CD34(B)-D17(G1 culture method)


title: Expt 7 - DonorC-eosinophil

value: eosinophils purified to average of 99%


title: Expt 7 - DonorC-pDC


title: Expt 9 - DonorE-eosinophil


title: Expt 8 - DonorD-eosinophil


title: Expt 8 - DonorD-basophil


title: Expt 1 - CD34(A)-D17(G3 culture method)


title: Expt 7 - DonorC-basophil